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colvarscript_commands.h File Reference

#include "colvarscript_commands_colvar.h"
#include "colvarscript_commands_bias.h"

Go to the source code of this file.

Defines

#define CVSCRIPT_COMM_FNAME(COMM)   cvscript_ ## COMM
#define CVSCRIPT_COMM_FNAME(COMM)   cvscript_ ## COMM
#define CVSCRIPT_COMM_PROTO(COMM)   int CVSCRIPT_COMM_FNAME(COMM)(void *, int, unsigned char *const *);
#define CVSCRIPT(COMM, HELP, N_ARGS_MIN, N_ARGS_MAX, ARGS, FN_BODY)   CVSCRIPT_COMM_PROTO(COMM)

Functions

int cvscript_n_commands ()
 Get the number of colvarscript commands. More...

char const ** cvscript_command_names ()
 Get the names of all commands (array of strings). More...

char const * cvscript_command_help (char const *cmd)
 Get the help summary of the given command
Parameters:
cmd  Name of the command's function (e.g. "cv_units").
 More...

char const * cvscript_command_rethelp (char const *cmd)
 Get description of the return value of a command
Parameters:
cmd  Name of the command's function (e.g. "cv_units").
 More...

char const * cvscript_command_arghelp (char const *cmd, int i)
 Get description of the arguments of a command (excluding prefix)
Parameters:
cmd  Name of the command's function (e.g. "cv_units")
i  Index of the argument; 0 is the first argument after the prefix, e.g. "value" has an index of 0 in the array of arguments: { "cv", "colvar", "xi", "value" }.
 More...

char const * cvscript_command_full_help (char const *cmd)
 Get the full help string of a command
Parameters:
cmd  Name of the command's function (e.g. "cv_units").
 More...

int cvscript_command_n_args_min (char const *cmd)
 Get number of required arguments (excluding prefix)
Parameters:
cmd  Name of the command's function (e.g. "cv_units").
 More...

int cvscript_command_n_args_max (char const *cmd)
 Get number of total arguments (excluding prefix)
Parameters:
cmd  Name of the command's function (e.g. "cv_units").
 More...

 CVSCRIPT (cv_addenergy,"Add an energy to the MD engine(no effect in VMD)", 1, 1,"E:float-Amount of energy to add", char const *Earg=script->obj_to_str(script->get_module_cmd_arg(0, objc, objv));cvm::main()->total_bias_energy+=strtod(Earg, NULL);return cvm::get_error();) CVSCRIPT(cv_bias
 CVSCRIPT (cv_colvar,"Prefix for colvar-specific commands", 0, 0,"", return COLVARS_OK;) CVSCRIPT(cv_config

Variables

Prefix for bias specific commands
Prefix for bias specific return COLVARS_OK
Read configuration from the
given 		string
Read configuration from the
given 		conf

Define Documentation

#define CVSCRIPT (  COMM,
HELP,
N_ARGS_MIN,
N_ARGS_MAX,
ARGS,
FN_BODY    )     CVSCRIPT_COMM_PROTO(COMM)
 

Definition at line 59 of file colvarscript_commands.h.

#define CVSCRIPT_COMM_FNAME (  COMM    )     cvscript_ ## COMM
 

Definition at line 44 of file colvarscript_commands.h.

#define CVSCRIPT_COMM_FNAME (  COMM    )     cvscript_ ## COMM
 

Definition at line 44 of file colvarscript_commands.h.

#define CVSCRIPT_COMM_PROTO (  COMM    )     int CVSCRIPT_COMM_FNAME(COMM)(void *, int, unsigned char *const *);
 

Definition at line 55 of file colvarscript_commands.h.

Function Documentation

CVSCRIPT (  cv_colvar   ,
"Prefix for colvar-specific commands"   ,
0   ,
0   ,
""   ,
return COLVARS_OK;   
) 
 

CVSCRIPT (  cv_addenergy   ,
"Add an energy to the MD engine(no effect in VMD)"   ,
1   ,
1   ,
"E:float-Amount of energy to add"   ,
char const *    Earg = script-,
obj_to_str(script->get_module_cmd_arg(0, objc, objv));cvm::main()-   ,
total_bias_energy+    = strtod(Earg, NULL); return cvm::get_error();
) 
 

char const* cvscript_command_arghelp (  char const *    cmd,
int    i
) 
 

Get description of the arguments of a command (excluding prefix)

Parameters:
cmd  Name of the command's function (e.g. "cv_units")
i  Index of the argument; 0 is the first argument after the prefix, e.g. "value" has an index of 0 in the array of arguments: { "cv", "colvar", "xi", "value" }.

Definition at line 53 of file colvarscript_commands.C.

Referenced by cvscript_command_full_help.

char const* cvscript_command_full_help (  char const *    cmd ) 
 

Get the full help string of a command

Parameters:
cmd  Name of the command's function (e.g. "cv_units").

Definition at line 61 of file colvarscript_commands.C.

References cvscript_command_arghelp, cvscript_command_help, cvscript_command_n_args_max, cvscript_command_n_args_min, cvscript_command_names, cvscript_command_rethelp, and cvscript_n_commands.

char const* cvscript_command_help (  char const *    cmd ) 
 

Get the help summary of the given command

Parameters:
cmd  Name of the command's function (e.g. "cv_units").

Definition at line 37 of file colvarscript_commands.C.

Referenced by cvscript_command_full_help.

int cvscript_command_n_args_max (  char const *    cmd ) 
 

Get number of total arguments (excluding prefix)

Parameters:
cmd  Name of the command's function (e.g. "cv_units").

Definition at line 77 of file colvarscript_commands.C.

Referenced by cvscript_command_full_help.

int cvscript_command_n_args_min (  char const *    cmd ) 
 

Get number of required arguments (excluding prefix)

Parameters:
cmd  Name of the command's function (e.g. "cv_units").

Definition at line 69 of file colvarscript_commands.C.

Referenced by cvscript_command_full_help.

char const** cvscript_command_names (    ) 
 

Get the names of all commands (array of strings).

Definition at line 29 of file colvarscript_commands.C.

char const* cvscript_command_rethelp (  char const *    cmd ) 
 

Get description of the return value of a command

Parameters:
cmd  Name of the command's function (e.g. "cv_units").

Definition at line 45 of file colvarscript_commands.C.

Referenced by cvscript_command_full_help.

int cvscript_n_commands (    ) 
 

Get the number of colvarscript commands.

Definition at line 22 of file colvarscript_commands.C.

Variable Documentation

Prefix for bias specific return COLVARS_OK
 

Definition at line 115 of file colvarscript_commands.h.

Prefix for bias specific commands
 

Definition at line 115 of file colvarscript_commands.h.

Read configuration from the given conf
 

Definition at line 131 of file colvarscript_commands.h.

Referenced by colvarparse::_get_keyval_scalar_, colvarparse::_get_keyval_vector_, colvarproxy::add_config, colvar::alch_lambda::alch_lambda, colvar::alpha_angles::alpha_angles, colvar::angle::angle, colvar::aspathCV::aspathCV, colvar::azpathCV::azpathCV, colvar::CartesianBasedPath::CartesianBasedPath, colvarmodule::change_configuration, colvarbias_restraint_linear::change_configuration, colvarbias_restraint_harmonic::change_configuration, colvarbias_restraint_k::change_configuration, colvarbias_restraint_centers::change_configuration, colvarparse::check_ascii, colvarparse::check_braces, colvarparse::check_keywords, colvar::coordnum::coordnum, cuda_occupancy_multiatom, colvar::CVBasedPath::CVBasedPath, colvar::cvc::cvc, colvar::dipole_magnitude::dipole_magnitude, colvar::distance::distance, colvar::distance_inv::distance_inv, colvar::distance_xy::distance_xy, colvar::distance_z::distance_z, colvarmodule::energy_difference, colvarbias_restraint_linear::energy_difference, colvarbias_restraint_harmonic::energy_difference, colvar::euler_phi::euler_phi, colvar::euler_psi::euler_psi, colvar::euler_theta::euler_theta, colvarparse::get_key_string_multi_value, colvarparse::get_keyval, colvardeps::get_keyval_feature, colvar::gspath::gspath, colvar::gspathCV::gspathCV, colvar::gzpath::gzpath, colvar::gzpathCV::gzpathCV, colvar::map_total::init, colvar::euler_theta::init, colvar::euler_psi::init, colvar::euler_phi::init, colvar::spin_angle::init, colvar::tilt::init, colvar::orientation_proj::init, colvar::orientation_angle::init, colvar::orientation::init, colvar::cvc::init, colvarbias_restraint_histogram::init, colvarbias_restraint_linear::init, colvarbias_restraint_harmonic_walls::init, colvarbias_restraint_harmonic::init, colvarbias_restraint_k_moving::init, colvarbias_restraint_centers_moving::init, colvarbias_restraint_moving::init, colvarbias_restraint_k::init, colvarbias_restraint_centers::init, colvarbias_restraint::init, colvarbias_meta::init, colvarbias_reweightaMD::init, colvarbias_histogram::init, colvarbias_alb::init, colvarbias_abf::init, colvarbias_ti::init, colvarbias::init, colvar::init, colvar::init_components, colvar::init_custom_function, colvarbias_meta::init_ebmeta_params, colvar::init_extended_Lagrangian, colvar::init_grid_parameters, colvar::init_output_flags, colvarbias_meta::init_replicas_params, colvar::cvc::init_total_force_params, colvarbias_meta::init_well_tempered_params, colvarparse::key_lookup, colvar::linearCombination::linearCombination, colvar::map_total::map_total, colvar::neuralNetwork::neuralNetwork, colvar::orientation::orientation, colvar::orientation_angle::orientation_angle, colvar::parse_analysis, colvarmodule::parse_biases, colvarmodule::parse_colvars, colvarmodule::parse_config, colvarmodule::parse_global_params, colvar::cvc::parse_group, colvar_grid< size_t >::parse_params, colvar::polar_theta::polar_theta, colvarmodule::read_config_file, colvarmodule::read_config_string, colvar_grid< size_t >::read_restart, colvarbias::read_state, colvar::read_state, colvarbias_restraint_linear::set_state_params, colvarbias_restraint_harmonic_walls::set_state_params, colvarbias_restraint_harmonic::set_state_params, colvarbias_restraint_k_moving::set_state_params, colvarbias_restraint_centers_moving::set_state_params, colvarbias_restraint_moving::set_state_params, colvarbias_restraint::set_state_params, colvarbias_alb::set_state_params, colvarbias::set_state_params, simple_scalar_dist_functions, colvarparse::strip_values, colvar::update_cvc_config, and vmd_get_visual.

Read configuration from the given string
 

Definition at line 131 of file colvarscript_commands.h.

Referenced by colvarparse::_get_keyval_scalar_value_, _to_str_vector, colvarproxy_io::backup_file, colvar::calc_runave, colvarparse::colvarparse, get_attribute_index, colvarbias_ti::get_state_params, colvarbias_meta::hills_traj_file_name, colvar::init_custom_function, colvar::init_grid_parameters, colvarmodule::read_colvar, colvar_grid< size_t >::read_restart, colvarbias_meta::read_state_data, colvarmodule::setup_input, colvarmodule::setup_output, colvarbias_meta::setup_output, tcl_get_weights, tcl_graphics_text, colvarproxy_tcl::tcl_run_colvar_callback, colvarproxy_tcl::tcl_run_colvar_gradient_callback, colvarproxy_tcl::tcl_run_force_callback, colvarvalue::to_simple_string, colvarmodule::matrix2d::to_simple_string, colvarmodule::vector1d::to_simple_string, colvarmodule::to_str, colvarbias_meta::update_replicas_registry, colvarmodule::version, colvar::write_output_files, and colvarmodule::write_restart.

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